Create easy access JVL files/links for launching in Jalview Develop
Build: #74 was successful
Job: Default Job was successful
Build log
The build generated 1,507 lines of output.The output is too long and has been truncated to the last 1,000 lines. Download or view full build log
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-1641_JSON does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-1641_JSON-File-format does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-1807java2Script does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-1953_Archeopteryx_with_Jalview_2_11_2 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-1965_JAL-753_JAL-1427_relaxedIdMatch does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-1978_msagrid does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-2040_JAL-2137_phyre2 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-2055alternateFeatureColours does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-2094_colourInterface does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-2103 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-2136_phyre2_integration does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-2136_phyre2_integration_updated does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-2253ensemblGenomes does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-2351jmolExchange does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-2476dropFiles does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-250_hideredundantseqs does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-2909_bamImport2_11 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-2909_bamImport_2_11_2 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-3010ontologyFeatureSettings does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-3020attributeValuePrompting does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-3085_gnupdf does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-3417_sdppred_calcs does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-345_selectFromFind does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-3638_jumptonextindel does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-3641_phredfromfastq does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-4071_visibleFeaturesCounter does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-4159_adjustable_gapparams_in_nw does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-4219_extended_fasta_rna_ss does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-4220_showSymbolsBelowConsensusThresholdAsGaps does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-629_with_threads_NOT_PASSING_TESTS does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-666_exportoverview does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-722alignmentProperties does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-728alternateQuality does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-845linkedProteinDnaEditing does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-845splitPaneMergeDevelop does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/r2_11_2/JAL-3922_jmolSelectionHighlighting does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/r2_11_2_JAL-3829_3dbeacons does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/r2_11_2_JAL-3929_3dbeacons does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/r_2_11_2_JAL-819_undeleteAutoAnnotation does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/flakytests/JAL-4026_AlignViewportWaitforcalculations does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/hack/JAL-1617_workaround does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/improvement/JAL-3289_new_launch_screens does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/improvement/JAL-3384_Redirect_stdout_and_stdin_to_files does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/improvement/JAL-3393_Improved_DMG_background_image_beta_strand does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/improvement/JAL-3393_make_DMG_background_image_relative_path_in_DS_Store does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/improvement/JAL-3416_FlatLaf_3.2.1 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/improvement/JAL-3416_GTK_look_and_feel does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/improvement/JAL-3438_eclipse_java_code_formatting_as_a_gradle_task does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/improvement/JAL-3594_BG_and_UoD_logos_added does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/improvement/JAL-3594_added_subtle_grey_tesselating_logos_to_getdown_splashscreen does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/improvement/JAL-3728_icons_for_independent_jframes does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/improvement/JAL-3790_enable_copy_to_clipboard_of_getdown_splashscreen_text does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/improvement/JAL-3826_gradle_configuration_for_intellij_idea does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/improvement/JAL-3847_add_dependencies_reported_by_gradle_7 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/improvement/JAL-3847_some_attempts_to_set_gradle_and_groovy_versions does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/improvement/JAL-3848_slivka_0.8_updated_jslib does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/improvement/JAL-4054_Upgrade_to_install4j10 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/improvement/JAL-4064_M1_native_JRE_bundled_in_DMG does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/j2s/develop does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/j2s/develop-bh does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/j2s/develop-bh-2 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/j2s/develop-jim does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/j2s/develop-mungo does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/j2s/develop-toc does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/jalview-headless does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/jims/work_on_2_12/JAL-3664_hmmer_ux does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/kjvdh/features/CipresWebservices does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/kjvdh/features/PhylogenyViewer does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/kjvdh/features/PhylogenyViewer_tabbedsupport does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/kjvdh/features/forester does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/kjvdh/features/testing does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/merge/Ben_trying_out_JSdevelop_with_develop does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/merge/JAL-2136_phyre2_integration does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/merge/JAL-3187_JAL-3010 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/merge/JAL-3210_developToJSDevelop does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/merge/JAL-3628+JAL-3608+JAL-3609+JAL-3541+JAL-3633+Release_2_11_1_Branch does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/merge/JAL-3628+JAL-3608+JAL-3609+JAL-3541+Release_2_11_1_Branch does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/merge/JAL-845_JAL-1640 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/merged_2_11_2_0_to_2_12 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/mmw/JAL-3878-ws-overhaul does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/mmw/JAL-3954_ebi_phmmer does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/mmw/JAL-4139-multi-harmony-patch does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/mmw/bug/JAL-4241-annotation-alignment-fix does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/patch/JAL-1236_customClustalHeader does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/patch/JAL-2694_maptoallchainsworkaround does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/patch/JAL-2755_UniprotEnsemblSubnameWorkaround does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/patch/JAL-2914_relaxedGFFpragmas does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/patch/JAL-2996_JAL-3053_tildeBracketsPipesEtcAsGapChars does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/patch/JAL-3562_fixAlignmentPanelTest does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/patch/JAL-3584_cherrypickto-JAL-3676_2.11.1.1 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/patch/JAL-3626_gradle_refinementsfrom2111 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/patch/JAL-3794_X_is_a_dna_rna_base_too does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/patch/JAL-3821_ena_rna_moltype does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/patch/JAL-3847_gradleV7andV8Patches does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/patch/JAL-4079_scalability_bottlenecks does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/patch/JAL-4155_IdCanvas_getAlignPanel_fix does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/patch/JAL-4195_calcWorker_for_2_11_2_6 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/patch/JAL-4216_negative_startend does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/patch/JAL-4222_quit_with_gui_export_cli_args does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/patch/r2_11_2_6/JAL-2350_embl_xrefs_from_uniprot_version_consistency does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/releases/Release_2_10_1_Branch does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/releases/Release_2_10_2b1_Branch does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/releases/Release_2_10_Branch does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/releases/Release_2_11_2_Branch does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/releases/Release_2_9_1_Branch does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/reviews/features/JAL-2136_phyre2_integration_withJims does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/spike/GFF_as_first_class_filetype_improvements_JAL-4028/placeholders_get_additional_sequence_data does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/spike/JAL-2778_changelookandfeelOpaqueWindows does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/spike/JAL-3548_exampleRestServer does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/spike/JAL-3622_Scanner_swingjs_J212_merge does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/spike/JAL-3690_with_patched_j2s_v3_2_9_plugin does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/spike/JAL-3753_helphtmldupes does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/spike/JAL-3781_2d_scaling does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/spike/JAL-4047/JAL-4048_columns_in_sequenceID does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/spike/JAL-4055_retire_JDesktop does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/spike/clinvar does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/spike/javier_noseqhack does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/spike/jims/Release_2_12_alpha does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/spike/phyre2 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/spike/t_sne_paeMatrix does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/spikes/JAL-4113_javafx_with_Jalview_MSA does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/spikes/jim does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/spikes/kira does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/spikes/koen does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/spikes/mungo does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/spikes/phyre does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/spikes/thomas does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/spikes/toch does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/story/JAL-3588_Examples_folder_in_macOS_DMG_Finder_window does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/task/JAL-3042_remove_SimpleDocument_dependency does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/task/JAL-3059_updateJmolandSwingJS does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/task/JAL-3089annLabelsPopup does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/task/JAL-3130_Java_11_investigations-Ben-2-CHANGES_TO_DEPRECATED_CALLS does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/task/JAL-3193mergeEnsemblGenomes does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/task/JAL-3210_ben_testing_jalviewJS_building does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/task/JAL-3252_adapt_getdown_to_unpack_tgz_resource_files does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/task/JAL-3281_Automatic_installers_download_table_generation does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/task/JAL-3349_Support_cli_JRE_arguments_through_getdown does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/task/JAL-3594_getdown_launcher_style does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/task/JAL-3789_configurable_j2s_file_for_headless_transpile does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/task/JAL-3805_Remove_Old_Jalview_Uninstaller_application does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/task/JAL-3911_getdown_improvements does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/task/JAL-4001_Release_2_11_2_Branch_with_GA4_cherry_picked does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/task/JAL-4001_Release_2_11_2_Branch_with_Plausible does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/task/JAL-4001_firebase_test does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/task/JAL-4059_updateJmolandSwingJS does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/task/r2_11_2/JAL-3871_Jmol_dedup does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/tasks/JAL-3067_slivkaprep does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/test/JAL-2422_testing_on_linux does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/test/JAL-3416_setOpaque_true_test_with_JalviewInternalFrame does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/testing/JAL-3577_jalviewversion_autoset does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/trial_merge/develop/bug/JAL-247autoIdWidthSeqMarker does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/update/JAL-3066_updated_testng_2022-01-28 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/update/JAL-3949_update_code_to_use_log4j-2_directly does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/vamsasDemo does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/tags/Archived_Release_2_7 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/tags/Jalview_2_4_0b2 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/tags/Release_2_10_1 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/tags/Release_2_11_2_7 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/tags/Release_2_4_0 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/tags/Release_2_5_1 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/tags/Release_2_6_1 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/2_5_1_rna_merge does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/JAL-1260_droldan does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/JAL-1375_ncbiclient does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/JAL-1550_intermine-sequence-annotation-client does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/JAL-1562_help-documentation-system-refactoring does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/JAL-2739_2.10.2b1 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/JAL-3253-applet-113cc13-2019.08.28-js-optimizations does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/JAL-3253-applet-SwingJS-omnibus does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/JAL-3253-applet-test does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/JAL-3253_applet_omnibus-BH does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/JAL-3315_getdown_1_8_6_update does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/JAL-3368_JavaScript_colors does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/JAL-3437_load_project does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/JAL-3878-ws-overhaul does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/JAL-3878_web_services_overhaul does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/JAL-3878_web_services_overhaul_no_clover does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/JAL-3954_ebi_phmmer does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/JAL-4154-platform-specific-constants does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/JAL-429_phylip-file-support does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/JalScape/JAL-1332 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/Jalview-JS/20190123 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/Jalview-JS/JAL-3253-applet does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/Jalview-JS/JAL-3253-applet-JAL-3445_support_for_BSML does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/Jalview-JS/JAL-3253-applet-JAL-3453-TestNG-Desktop-getInstanceOnly does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/Jalview-JS/JAL-3253-applet-SwingJS-3.2.9.v1e does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/Jalview-JS/JAL-3560-bh-temp does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/Jalview-JS/JAL-3560_bob_temp does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/Jalview-JS/JAL-3563-sync-TestNG-test-bob does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/Jalview-JS/demo does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/Jalview-JS/develop-JAL-3559 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/Jalview-JS/develop-updated-gradle does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/Jalview-JS/develop.JAL-3446.SequenceFeatureAsync does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/Jalview-JS/develop.JAL-3446.ctrlDown does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/Jalview-JS/gradle-minimal does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/Jalview-JS/gradle_with_goomph does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/Jalview-JS/gradle_with_inline_eclipse does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/Jalview-JS/jim/JAL-3253-JAL-3418 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/Jalview-JS/update_java2script does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/Jalview-jJS/JAL-3253-applet-JAL-3436 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/Pre_R29_develop does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/RNAalifold does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/Release_2_3_BuildFix does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/Release_2_4_branch does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/Release_2_5_Branch does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/Release_2_6_Branch does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/Release_2_7_Branch does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/Release_2_8_1_Branch_i18n does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/Release_2_8_2_Branch_i18n does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/Release_2_8_2b1_Branch does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/Release_2_9_0b1_Branch does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/Release_2_9_Branch does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/Tcoffee_JAL-1065 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/VamJalview does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/alpha/Jalview_212_test_merged_buildgradle does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/arnaud/JAL-3929_spike does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-1644_Finder-logic-improvement does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-1712annotationsWithFlanking does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-1988_quit_window_focus does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-2023_cdsProjectError does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-2339helpBullets does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-247autoIdWidthSeqMarker does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-2541_JAL-2823_cutAndRelocateFeatures_needs_merge_from_211_release does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-2791selectVisibleFeatures does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-2848resetColoursAmendFeatures does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-2876byLabelThreshold does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-2907stockholmGapChar does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-3003epsWithSelection does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-3059groupBorder does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-3083cancelAnnotationColour does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-3088_RNA_secondary_structure_annotation_final-ending-solo-brace_arrow_points_the_wrong_way does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-3178nonposFeatureExport_take2 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-3183groupColourOverwritten does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-3184restoreGroupVisibility does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-3195idResolution does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-3201groupClustal does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-3202zerosInProfile does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-3212columnSelectionWithHidden does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-3215hydroColours does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-3235sortPropertiesJava9 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-3235sortPropertiesJava9-2 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-3288_override_all_JInternalFrame_with_Classic_JInternalFrame does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-3365_failing_per_sequence_ss_tests does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-3473_SpinnerNumberModel_causing_IllegalArgumentException does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-3487-splash-JS does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-3489mapChainsFromFile does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-3490findSpanHiddenGaps does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-3502wrappedScale does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-360+JAL-3975_keyboard_input_lost_after_dialog does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-3609_HiDPI_in_Linux does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-360_JAL-3984_F2_stops_working_after_some_dialogs does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-3613emblCDSTracking does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-3633_Allow_HTTPS_proxy_configuration_for_getdown does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-3648graphDragRelease does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-3702_Drag_and_drop_miscalculation_in_linux_HiDPI does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-3705saveProteinId does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-3706virtualStopCodon does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-3725overlappingVirtualFeatures does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-3744_read_gzip_file_in_jalviewjs does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-3751_revisited does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-3751overlappingCDS does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-3761_locateInFromTo does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-3774_splitFrameFinder does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-3779setGroupProperties does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-3788_autoOverviewClustal does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-3972_VAqua_for_Java11 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-3975_keyboard_input_stops_working_after_create_sequence_feature does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-4026_fix_failingSeqPanel does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-4041_no_3dbeacons_when_no_uniprotseq does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-4041_problems_with_3dbeacons_search does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-4072_zip_slip_vulnerability_in_getdown does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-4073_pfam_website_being_decommissioned does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-4118_Fix_QuitHandlerTest does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-4153_JvCacheableInputBoxTest_flaky_on_build_server does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-4225_rnaalifold_structure_not_recognised_as_such does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-4229_varna_helix_mapping_offby1 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-4290_headless_alignment_export_with_structure_annotations_doesnt_include_secondary_structure_and_temperature_factor does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-4353_cannot_output_multiple_different_structure_images_for_one_alignment does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-4353_cannot_output_multiple_different_structure_images_for_one_alignment_with_renderpatch does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-4369_uniprot_in_jalviewJS does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-4374_missing_colon_when_using_jalview_scheme_with_host_and_port does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-4389-web-services-prefs-panel does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/cherry-pick/JAL-3621_to_Release_2_11_1_Branch does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/cherry-pick/JAL-3691_to_2.11.2_localeSafeFileImport does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/codereviews/JAL-1990_IProgressIndicator_jalview.structure does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/development/JAL-3878_ws_overhaul_3_merged_with_2_12_Merged does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/feature/JAL-1260_genbank_embl_flatfile_import_reloaded does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/feature/JAL-2087ensemblSpeciesAssist does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/feature/JAL-2422ChimeraX does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/feature/JAL-2611 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/feature/JAL-2674take2 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/feature/JAL-2738GeneLocus does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/feature/JAL-2873ensemblSpeciesQuery does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/feature/JAL-2909bamfiles does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/feature/JAL-2909bamfiles_features does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/feature/JAL-3081customAnnOrder does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/feature/JAL-3117_overviewFocusAlignment does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/feature/JAL-3148structureColourSchemes does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/feature/JAL-3187viewstyleFlags does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/feature/JAL-3190jalviewjsChimera does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/feature/JAL-3194_create_launcher_with_dynamic_memory_heap_setting does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/feature/JAL-3251biotypedMappings does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/feature/JAL-3364splitFrameImage does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/feature/JAL-3390hideUnmappedStructure does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/feature/JAL-3400viewChainsMenu does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/feature/JAL-3442colourCaching does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/feature/JAL-3443findColorAsInt does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/feature/JAL-3469clinvarVCF does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/feature/JAL-3481_conservation_gap_threshold_preferences does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/feature/JAL-3499featuresFileMotifs does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/feature/JAL-3719_gapColourInAlignmentView does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/feature/JAL-3719_gapColourInAlignmentView_2.11.2 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/feature/JAL-3730ensemblPingRetries does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/feature/JAL-3739_useFormFieldText does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/feature/JAL-3851_prototype_comms_for_jbrowse2 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/feature/JAL-3851_rest_api_for_genome_browser does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/feature/JAL-3851_rest_api_for_genome_browser_updated_with_develop does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/feature/JAL-3874_add_source_jars_to_eclipse does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/feature/JAL-3982_mouseover_highlighting_viaJAL-3860 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/feature/JAL-4227_Rfam2020_sslines does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/feature/JAL-4392_consensus_secondary_structure does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/feature/JAL-819undeleteAutoannotation does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/feature/r2_11_2/JAL-3808_gff2_exonerate does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-1499 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-1499_MEGA does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-1550_intermine-sequence-annotation-client does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-1601_jpred4rest does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-161_JAL-4172_nhx_tags_in_stockholm does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-161_JAL-4173_nhx_tags_in_stockholm does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-1641_JSON does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-1641_JSON-File-format does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-1807java2Script does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-1953_Archeopteryx_with_Jalview_2_11_2 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-1965_JAL-753_JAL-1427_relaxedIdMatch does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-1978_msagrid does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-2040_JAL-2137_phyre2 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-2055alternateFeatureColours does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-2094_colourInterface does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-2103 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-2136_phyre2_integration does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-2136_phyre2_integration_updated does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-2253ensemblGenomes does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-2351jmolExchange does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-2476dropFiles does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-250_hideredundantseqs does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-2909_bamImport2_11 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-2909_bamImport_2_11_2 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-3010ontologyFeatureSettings does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-3020attributeValuePrompting does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-3085_gnupdf does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-3417_sdppred_calcs does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-345_selectFromFind does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-3638_jumptonextindel does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-3641_phredfromfastq does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-4071_visibleFeaturesCounter does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-4159_adjustable_gapparams_in_nw does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-4219_extended_fasta_rna_ss does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-4220_showSymbolsBelowConsensusThresholdAsGaps does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-629_with_threads_NOT_PASSING_TESTS does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-666_exportoverview does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-722alignmentProperties does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-728alternateQuality does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-845linkedProteinDnaEditing does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-845splitPaneMergeDevelop does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/r2_11_2/JAL-3922_jmolSelectionHighlighting does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/r2_11_2_JAL-3829_3dbeacons does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/r2_11_2_JAL-3929_3dbeacons does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/r_2_11_2_JAL-819_undeleteAutoAnnotation does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/flakytests/JAL-4026_AlignViewportWaitforcalculations does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/hack/JAL-1617_workaround does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/improvement/JAL-3289_new_launch_screens does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/improvement/JAL-3384_Redirect_stdout_and_stdin_to_files does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/improvement/JAL-3393_Improved_DMG_background_image_beta_strand does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/improvement/JAL-3393_make_DMG_background_image_relative_path_in_DS_Store does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/improvement/JAL-3416_FlatLaf_3.2.1 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/improvement/JAL-3416_GTK_look_and_feel does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/improvement/JAL-3438_eclipse_java_code_formatting_as_a_gradle_task does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/improvement/JAL-3594_BG_and_UoD_logos_added does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/improvement/JAL-3594_added_subtle_grey_tesselating_logos_to_getdown_splashscreen does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/improvement/JAL-3728_icons_for_independent_jframes does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/improvement/JAL-3790_enable_copy_to_clipboard_of_getdown_splashscreen_text does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/improvement/JAL-3826_gradle_configuration_for_intellij_idea does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/improvement/JAL-3847_add_dependencies_reported_by_gradle_7 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/improvement/JAL-3847_some_attempts_to_set_gradle_and_groovy_versions does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/improvement/JAL-3848_slivka_0.8_updated_jslib does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/improvement/JAL-4054_Upgrade_to_install4j10 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/improvement/JAL-4064_M1_native_JRE_bundled_in_DMG does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/j2s/develop does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/j2s/develop-bh does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/j2s/develop-bh-2 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/j2s/develop-jim does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/j2s/develop-mungo does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/j2s/develop-toc does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/jalview-headless does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/jims/work_on_2_12/JAL-3664_hmmer_ux does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/kjvdh/features/CipresWebservices does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/kjvdh/features/PhylogenyViewer does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/kjvdh/features/PhylogenyViewer_tabbedsupport does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/kjvdh/features/forester does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/kjvdh/features/testing does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/merge/Ben_trying_out_JSdevelop_with_develop does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/merge/JAL-2136_phyre2_integration does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/merge/JAL-3187_JAL-3010 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/merge/JAL-3210_developToJSDevelop does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/merge/JAL-3628+JAL-3608+JAL-3609+JAL-3541+JAL-3633+Release_2_11_1_Branch does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/merge/JAL-3628+JAL-3608+JAL-3609+JAL-3541+Release_2_11_1_Branch does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/merge/JAL-845_JAL-1640 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/merged_2_11_2_0_to_2_12 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/mmw/JAL-3878-ws-overhaul does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/mmw/JAL-3954_ebi_phmmer does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/mmw/JAL-4139-multi-harmony-patch does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/mmw/bug/JAL-4241-annotation-alignment-fix does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/patch/JAL-1236_customClustalHeader does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/patch/JAL-2694_maptoallchainsworkaround does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/patch/JAL-2755_UniprotEnsemblSubnameWorkaround does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/patch/JAL-2914_relaxedGFFpragmas does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/patch/JAL-2996_JAL-3053_tildeBracketsPipesEtcAsGapChars does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/patch/JAL-3562_fixAlignmentPanelTest does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/patch/JAL-3584_cherrypickto-JAL-3676_2.11.1.1 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/patch/JAL-3626_gradle_refinementsfrom2111 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/patch/JAL-3794_X_is_a_dna_rna_base_too does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/patch/JAL-3821_ena_rna_moltype does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/patch/JAL-3847_gradleV7andV8Patches does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/patch/JAL-4079_scalability_bottlenecks does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/patch/JAL-4155_IdCanvas_getAlignPanel_fix does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/patch/JAL-4195_calcWorker_for_2_11_2_6 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/patch/JAL-4216_negative_startend does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/patch/JAL-4222_quit_with_gui_export_cli_args does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/patch/r2_11_2_6/JAL-2350_embl_xrefs_from_uniprot_version_consistency does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/releases/Release_2_10_1_Branch does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/releases/Release_2_10_2b1_Branch does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/releases/Release_2_10_Branch does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/releases/Release_2_11_2_Branch does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/releases/Release_2_9_1_Branch does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/reviews/features/JAL-2136_phyre2_integration_withJims does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/spike/GFF_as_first_class_filetype_improvements_JAL-4028/placeholders_get_additional_sequence_data does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/spike/JAL-2778_changelookandfeelOpaqueWindows does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/spike/JAL-3548_exampleRestServer does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/spike/JAL-3622_Scanner_swingjs_J212_merge does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/spike/JAL-3690_with_patched_j2s_v3_2_9_plugin does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/spike/JAL-3753_helphtmldupes does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/spike/JAL-3781_2d_scaling does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/spike/JAL-4047/JAL-4048_columns_in_sequenceID does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/spike/JAL-4055_retire_JDesktop does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/spike/clinvar does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/spike/javier_noseqhack does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/spike/jims/Release_2_12_alpha does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/spike/phyre2 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/spike/t_sne_paeMatrix does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/spikes/JAL-4113_javafx_with_Jalview_MSA does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/spikes/jim does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/spikes/kira does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/spikes/koen does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/spikes/mungo does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/spikes/phyre does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/spikes/thomas does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/spikes/toch does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/story/JAL-3588_Examples_folder_in_macOS_DMG_Finder_window does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/task/JAL-3042_remove_SimpleDocument_dependency does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/task/JAL-3059_updateJmolandSwingJS does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/task/JAL-3089annLabelsPopup does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/task/JAL-3130_Java_11_investigations-Ben-2-CHANGES_TO_DEPRECATED_CALLS does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/task/JAL-3193mergeEnsemblGenomes does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/task/JAL-3210_ben_testing_jalviewJS_building does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/task/JAL-3252_adapt_getdown_to_unpack_tgz_resource_files does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/task/JAL-3281_Automatic_installers_download_table_generation does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/task/JAL-3349_Support_cli_JRE_arguments_through_getdown does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/task/JAL-3594_getdown_launcher_style does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/task/JAL-3789_configurable_j2s_file_for_headless_transpile does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/task/JAL-3805_Remove_Old_Jalview_Uninstaller_application does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/task/JAL-3911_getdown_improvements does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/task/JAL-4001_Release_2_11_2_Branch_with_GA4_cherry_picked does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/task/JAL-4001_Release_2_11_2_Branch_with_Plausible does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/task/JAL-4001_firebase_test does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/task/JAL-4059_updateJmolandSwingJS does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/task/r2_11_2/JAL-3871_Jmol_dedup does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/tasks/JAL-3067_slivkaprep does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/test/JAL-2422_testing_on_linux does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/test/JAL-3416_setOpaque_true_test_with_JalviewInternalFrame does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/testing/JAL-3577_jalviewversion_autoset does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/trial_merge/develop/bug/JAL-247autoIdWidthSeqMarker does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/update/JAL-3066_updated_testng_2022-01-28 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/update/JAL-3949_update_code_to_use_log4j-2_directly does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/vamsasDemo does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/tags/Archived_Release_2_7 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/tags/Jalview_2_4_0b2 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/tags/Release_2_10_1 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/tags/Release_2_11_2_7 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/tags/Release_2_4_0 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/tags/Release_2_5_1 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/tags/Release_2_6_1 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/2_5_1_rna_merge does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/JAL-1260_droldan does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/JAL-1375_ncbiclient does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/JAL-1550_intermine-sequence-annotation-client does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/JAL-1562_help-documentation-system-refactoring does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/JAL-2739_2.10.2b1 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/JAL-3253-applet-113cc13-2019.08.28-js-optimizations does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/JAL-3253-applet-SwingJS-omnibus does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/JAL-3253-applet-test does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/JAL-3253_applet_omnibus-BH does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/JAL-3315_getdown_1_8_6_update does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/JAL-3368_JavaScript_colors does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/JAL-3437_load_project does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/JAL-3878-ws-overhaul does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/JAL-3878_web_services_overhaul does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/JAL-3878_web_services_overhaul_no_clover does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/JAL-3954_ebi_phmmer does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/JAL-4154-platform-specific-constants does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/JAL-429_phylip-file-support does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/JalScape/JAL-1332 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/Jalview-JS/20190123 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/Jalview-JS/JAL-3253-applet does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/Jalview-JS/JAL-3253-applet-JAL-3445_support_for_BSML does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/Jalview-JS/JAL-3253-applet-JAL-3453-TestNG-Desktop-getInstanceOnly does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/Jalview-JS/JAL-3253-applet-SwingJS-3.2.9.v1e does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/Jalview-JS/JAL-3560-bh-temp does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/Jalview-JS/JAL-3560_bob_temp does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/Jalview-JS/JAL-3563-sync-TestNG-test-bob does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/Jalview-JS/demo does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/Jalview-JS/develop-JAL-3559 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/Jalview-JS/develop-updated-gradle does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/Jalview-JS/develop.JAL-3446.SequenceFeatureAsync does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/Jalview-JS/develop.JAL-3446.ctrlDown does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/Jalview-JS/gradle-minimal does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/Jalview-JS/gradle_with_goomph does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/Jalview-JS/gradle_with_inline_eclipse does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/Jalview-JS/jim/JAL-3253-JAL-3418 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/Jalview-JS/update_java2script does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/Jalview-jJS/JAL-3253-applet-JAL-3436 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/Pre_R29_develop does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/RNAalifold does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/Release_2_3_BuildFix does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/Release_2_4_branch does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/Release_2_5_Branch does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/Release_2_6_Branch does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/Release_2_7_Branch does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/Release_2_8_1_Branch_i18n does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/Release_2_8_2_Branch_i18n does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/Release_2_8_2b1_Branch does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/Release_2_9_0b1_Branch does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/Release_2_9_Branch does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/Tcoffee_JAL-1065 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/VamJalview does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/alpha/Jalview_212_test_merged_buildgradle does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/arnaud/JAL-3929_spike does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-1644_Finder-logic-improvement does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-1712annotationsWithFlanking does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-1988_quit_window_focus does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-2023_cdsProjectError does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-2339helpBullets does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-247autoIdWidthSeqMarker does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-2541_JAL-2823_cutAndRelocateFeatures_needs_merge_from_211_release does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-2791selectVisibleFeatures does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-2848resetColoursAmendFeatures does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-2876byLabelThreshold does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-2907stockholmGapChar does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-3003epsWithSelection does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-3059groupBorder does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-3083cancelAnnotationColour does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-3088_RNA_secondary_structure_annotation_final-ending-solo-brace_arrow_points_the_wrong_way does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-3178nonposFeatureExport_take2 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-3183groupColourOverwritten does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-3184restoreGroupVisibility does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-3195idResolution does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-3201groupClustal does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-3202zerosInProfile does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-3212columnSelectionWithHidden does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-3215hydroColours does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-3235sortPropertiesJava9 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-3235sortPropertiesJava9-2 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-3288_override_all_JInternalFrame_with_Classic_JInternalFrame does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-3365_failing_per_sequence_ss_tests does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-3473_SpinnerNumberModel_causing_IllegalArgumentException does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-3487-splash-JS does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-3489mapChainsFromFile does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-3490findSpanHiddenGaps does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-3502wrappedScale does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-360+JAL-3975_keyboard_input_lost_after_dialog does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-3609_HiDPI_in_Linux does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-360_JAL-3984_F2_stops_working_after_some_dialogs does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-3613emblCDSTracking does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-3633_Allow_HTTPS_proxy_configuration_for_getdown does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-3648graphDragRelease does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-3702_Drag_and_drop_miscalculation_in_linux_HiDPI does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-3705saveProteinId does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-3706virtualStopCodon does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-3725overlappingVirtualFeatures does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-3744_read_gzip_file_in_jalviewjs does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-3751_revisited does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-3751overlappingCDS does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-3761_locateInFromTo does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-3774_splitFrameFinder does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-3779setGroupProperties does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-3788_autoOverviewClustal does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-3972_VAqua_for_Java11 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-3975_keyboard_input_stops_working_after_create_sequence_feature does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-4026_fix_failingSeqPanel does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-4041_no_3dbeacons_when_no_uniprotseq does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-4041_problems_with_3dbeacons_search does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-4072_zip_slip_vulnerability_in_getdown does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-4073_pfam_website_being_decommissioned does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-4118_Fix_QuitHandlerTest does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-4153_JvCacheableInputBoxTest_flaky_on_build_server does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-4225_rnaalifold_structure_not_recognised_as_such does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-4229_varna_helix_mapping_offby1 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-4290_headless_alignment_export_with_structure_annotations_doesnt_include_secondary_structure_and_temperature_factor does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-4353_cannot_output_multiple_different_structure_images_for_one_alignment does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-4353_cannot_output_multiple_different_structure_images_for_one_alignment_with_renderpatch does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-4369_uniprot_in_jalviewJS does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-4374_missing_colon_when_using_jalview_scheme_with_host_and_port does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/bug/JAL-4389-web-services-prefs-panel does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/cherry-pick/JAL-3621_to_Release_2_11_1_Branch does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/cherry-pick/JAL-3691_to_2.11.2_localeSafeFileImport does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/codereviews/JAL-1990_IProgressIndicator_jalview.structure does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/development/JAL-3878_ws_overhaul_3_merged_with_2_12_Merged does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/feature/JAL-1260_genbank_embl_flatfile_import_reloaded does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/feature/JAL-2087ensemblSpeciesAssist does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/feature/JAL-2422ChimeraX does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/feature/JAL-2611 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/feature/JAL-2674take2 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/feature/JAL-2738GeneLocus does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/feature/JAL-2873ensemblSpeciesQuery does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/feature/JAL-2909bamfiles does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/feature/JAL-2909bamfiles_features does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/feature/JAL-3081customAnnOrder does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/feature/JAL-3117_overviewFocusAlignment does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/feature/JAL-3148structureColourSchemes does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/feature/JAL-3187viewstyleFlags does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/feature/JAL-3190jalviewjsChimera does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/feature/JAL-3194_create_launcher_with_dynamic_memory_heap_setting does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/feature/JAL-3251biotypedMappings does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/feature/JAL-3364splitFrameImage does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/feature/JAL-3390hideUnmappedStructure does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/feature/JAL-3400viewChainsMenu does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/feature/JAL-3442colourCaching does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/feature/JAL-3443findColorAsInt does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/feature/JAL-3469clinvarVCF does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/feature/JAL-3481_conservation_gap_threshold_preferences does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/feature/JAL-3499featuresFileMotifs does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/feature/JAL-3719_gapColourInAlignmentView does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/feature/JAL-3719_gapColourInAlignmentView_2.11.2 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/feature/JAL-3730ensemblPingRetries does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/feature/JAL-3739_useFormFieldText does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/feature/JAL-3851_prototype_comms_for_jbrowse2 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/feature/JAL-3851_rest_api_for_genome_browser does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/feature/JAL-3851_rest_api_for_genome_browser_updated_with_develop does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/feature/JAL-3874_add_source_jars_to_eclipse does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/feature/JAL-3982_mouseover_highlighting_viaJAL-3860 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/feature/JAL-4227_Rfam2020_sslines does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/feature/JAL-4392_consensus_secondary_structure does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/feature/JAL-819undeleteAutoannotation does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/feature/r2_11_2/JAL-3808_gff2_exonerate does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-1499 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-1499_MEGA does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-1550_intermine-sequence-annotation-client does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-1601_jpred4rest does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-161_JAL-4172_nhx_tags_in_stockholm does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-161_JAL-4173_nhx_tags_in_stockholm does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-1641_JSON does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-1641_JSON-File-format does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-1807java2Script does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-1953_Archeopteryx_with_Jalview_2_11_2 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-1965_JAL-753_JAL-1427_relaxedIdMatch does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-1978_msagrid does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-2040_JAL-2137_phyre2 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-2055alternateFeatureColours does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-2094_colourInterface does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-2103 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-2136_phyre2_integration does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-2136_phyre2_integration_updated does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-2253ensemblGenomes does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-2351jmolExchange does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-2476dropFiles does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-250_hideredundantseqs does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-2909_bamImport2_11 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-2909_bamImport_2_11_2 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-3010ontologyFeatureSettings does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-3020attributeValuePrompting does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-3085_gnupdf does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-3417_sdppred_calcs does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-345_selectFromFind does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-3638_jumptonextindel does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-3641_phredfromfastq does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-4071_visibleFeaturesCounter does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-4159_adjustable_gapparams_in_nw does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-4219_extended_fasta_rna_ss does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-4220_showSymbolsBelowConsensusThresholdAsGaps does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-629_with_threads_NOT_PASSING_TESTS does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-666_exportoverview does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-722alignmentProperties does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-728alternateQuality does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-845linkedProteinDnaEditing does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/JAL-845splitPaneMergeDevelop does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/r2_11_2/JAL-3922_jmolSelectionHighlighting does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/r2_11_2_JAL-3829_3dbeacons does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/r2_11_2_JAL-3929_3dbeacons does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/features/r_2_11_2_JAL-819_undeleteAutoAnnotation does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/flakytests/JAL-4026_AlignViewportWaitforcalculations does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/hack/JAL-1617_workaround does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/improvement/JAL-3289_new_launch_screens does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/improvement/JAL-3384_Redirect_stdout_and_stdin_to_files does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/improvement/JAL-3393_Improved_DMG_background_image_beta_strand does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/improvement/JAL-3393_make_DMG_background_image_relative_path_in_DS_Store does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/improvement/JAL-3416_FlatLaf_3.2.1 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/improvement/JAL-3416_GTK_look_and_feel does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/improvement/JAL-3438_eclipse_java_code_formatting_as_a_gradle_task does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/improvement/JAL-3594_BG_and_UoD_logos_added does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/improvement/JAL-3594_added_subtle_grey_tesselating_logos_to_getdown_splashscreen does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/improvement/JAL-3728_icons_for_independent_jframes does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/improvement/JAL-3790_enable_copy_to_clipboard_of_getdown_splashscreen_text does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/improvement/JAL-3826_gradle_configuration_for_intellij_idea does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/improvement/JAL-3847_add_dependencies_reported_by_gradle_7 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/improvement/JAL-3847_some_attempts_to_set_gradle_and_groovy_versions does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/improvement/JAL-3848_slivka_0.8_updated_jslib does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/improvement/JAL-4054_Upgrade_to_install4j10 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/improvement/JAL-4064_M1_native_JRE_bundled_in_DMG does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/j2s/develop does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/j2s/develop-bh does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/j2s/develop-bh-2 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/j2s/develop-jim does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/j2s/develop-mungo does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/j2s/develop-toc does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/jalview-headless does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/jims/work_on_2_12/JAL-3664_hmmer_ux does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/kjvdh/features/CipresWebservices does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/kjvdh/features/PhylogenyViewer does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/kjvdh/features/PhylogenyViewer_tabbedsupport does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/kjvdh/features/forester does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/kjvdh/features/testing does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/merge/Ben_trying_out_JSdevelop_with_develop does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/merge/JAL-2136_phyre2_integration does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/merge/JAL-3187_JAL-3010 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/merge/JAL-3210_developToJSDevelop does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/merge/JAL-3628+JAL-3608+JAL-3609+JAL-3541+JAL-3633+Release_2_11_1_Branch does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/merge/JAL-3628+JAL-3608+JAL-3609+JAL-3541+Release_2_11_1_Branch does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/merge/JAL-845_JAL-1640 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/merged_2_11_2_0_to_2_12 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/mmw/JAL-3878-ws-overhaul does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/mmw/JAL-3954_ebi_phmmer does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/mmw/JAL-4139-multi-harmony-patch does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/mmw/bug/JAL-4241-annotation-alignment-fix does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/patch/JAL-1236_customClustalHeader does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/patch/JAL-2694_maptoallchainsworkaround does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/patch/JAL-2755_UniprotEnsemblSubnameWorkaround does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/patch/JAL-2914_relaxedGFFpragmas does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/patch/JAL-2996_JAL-3053_tildeBracketsPipesEtcAsGapChars does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/patch/JAL-3562_fixAlignmentPanelTest does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/patch/JAL-3584_cherrypickto-JAL-3676_2.11.1.1 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/patch/JAL-3626_gradle_refinementsfrom2111 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/patch/JAL-3794_X_is_a_dna_rna_base_too does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/patch/JAL-3821_ena_rna_moltype does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/patch/JAL-3847_gradleV7andV8Patches does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/patch/JAL-4079_scalability_bottlenecks does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/patch/JAL-4155_IdCanvas_getAlignPanel_fix does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/patch/JAL-4195_calcWorker_for_2_11_2_6 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/patch/JAL-4216_negative_startend does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/patch/JAL-4222_quit_with_gui_export_cli_args does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/patch/r2_11_2_6/JAL-2350_embl_xrefs_from_uniprot_version_consistency does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/releases/Release_2_10_1_Branch does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/releases/Release_2_10_2b1_Branch does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/releases/Release_2_10_Branch does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/releases/Release_2_11_2_Branch does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/releases/Release_2_9_1_Branch does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/reviews/features/JAL-2136_phyre2_integration_withJims does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/spike/GFF_as_first_class_filetype_improvements_JAL-4028/placeholders_get_additional_sequence_data does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/spike/JAL-2778_changelookandfeelOpaqueWindows does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/spike/JAL-3548_exampleRestServer does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/spike/JAL-3622_Scanner_swingjs_J212_merge does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/spike/JAL-3690_with_patched_j2s_v3_2_9_plugin does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/spike/JAL-3753_helphtmldupes does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/spike/JAL-3781_2d_scaling does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/spike/JAL-4047/JAL-4048_columns_in_sequenceID does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/spike/JAL-4055_retire_JDesktop does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/spike/clinvar does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/spike/javier_noseqhack does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/spike/jims/Release_2_12_alpha does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/spike/phyre2 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/spike/t_sne_paeMatrix does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/spikes/JAL-4113_javafx_with_Jalview_MSA does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/spikes/jim does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/spikes/kira does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/spikes/koen does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/spikes/mungo does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/spikes/phyre does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/spikes/thomas does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/spikes/toch does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/story/JAL-3588_Examples_folder_in_macOS_DMG_Finder_window does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/task/JAL-3042_remove_SimpleDocument_dependency does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/task/JAL-3059_updateJmolandSwingJS does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/task/JAL-3089annLabelsPopup does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/task/JAL-3130_Java_11_investigations-Ben-2-CHANGES_TO_DEPRECATED_CALLS does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/task/JAL-3193mergeEnsemblGenomes does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/task/JAL-3210_ben_testing_jalviewJS_building does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/task/JAL-3252_adapt_getdown_to_unpack_tgz_resource_files does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/task/JAL-3281_Automatic_installers_download_table_generation does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/task/JAL-3349_Support_cli_JRE_arguments_through_getdown does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/task/JAL-3594_getdown_launcher_style does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/task/JAL-3789_configurable_j2s_file_for_headless_transpile does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/task/JAL-3805_Remove_Old_Jalview_Uninstaller_application does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/task/JAL-3911_getdown_improvements does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/task/JAL-4001_Release_2_11_2_Branch_with_GA4_cherry_picked does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/task/JAL-4001_Release_2_11_2_Branch_with_Plausible does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/task/JAL-4001_firebase_test does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/task/JAL-4059_updateJmolandSwingJS does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/task/r2_11_2/JAL-3871_Jmol_dedup does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/tasks/JAL-3067_slivkaprep does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/test/JAL-2422_testing_on_linux does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/test/JAL-3416_setOpaque_true_test_with_JalviewInternalFrame does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/testing/JAL-3577_jalviewversion_autoset does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/trial_merge/develop/bug/JAL-247autoIdWidthSeqMarker does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/update/JAL-3066_updated_testng_2022-01-28 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/update/JAL-3949_update_code_to_use_log4j-2_directly does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/remotes/origin/vamsasDemo does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/tags/Archived_Release_2_7 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/tags/Jalview_2_4_0b2 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/tags/Release_2_10_1 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/tags/Release_2_11_2_7 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/tags/Release_2_4_0 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/tags/Release_2_5_1 does not point to a valid object! |
| 06-Feb-2025 11:24:25 | error: refs/tags/Release_2_6_1 does not point to a valid object! |
| 06-Feb-2025 11:24:27 | Already on 'develop' |
| 06-Feb-2025 11:24:27 | Updated source code to revision: 1dad9dc2f7ff8466ad11d8c945aaa9140748ef8a |
| 06-Feb-2025 11:24:27 | Finished task 'Checkout Default Repository' with result: Success |
| 06-Feb-2025 11:24:27 | Running pre-build action: VCS Version Collector |
| 06-Feb-2025 11:24:27 | Running pre-build action: Artifactory Release Staging |
| 06-Feb-2025 11:24:27 | Substituting variable: ${bamboo.planKey} with JB-GDL |
| 06-Feb-2025 11:24:27 | Starting task 'Jalview Develop Launcher JVL (Java 11)' of type 'org.jfrog.bamboo.bamboo-artifactory-plugin:artifactoryGradleTask' |
| 06-Feb-2025 11:24:27 | Bamboo Artifactory Plugin version: 2.6.2 |
| 06-Feb-2025 11:24:27 | Beginning to execute external process for build 'Jalview Builds - Getdown DEVELOP Launchers - Default Job #74 (JB-GDL-JOB1-74)' ... running command line: /home/bamboo/buildtools/gradle/bin/gradle -x test -PCHANNEL=BUILD -PJAVA_VERSION=11 -Pbamboo_planKey=JB-GDL -Pbamboo_buildResultsUrl=${bamboo_buildResultsUrl} -Pbamboo_buildResultKey=${bamboo_buildResultKey} clean getdown ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL-JOB1 ... using extra environment variables: bamboo_planRepository_1_branch=develop bamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr CATALINA_PID=/home/bamboo/latest/work/bamboo.pid bamboo_planRepository_1_branchDisplayName=develop bamboo_repository_revision_number=1dad9dc2f7ff8466ad11d8c945aaa9140748ef8a bamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDL-JOB1-74 JAVA_OPTS=-Xms512m -Xmx1024m -Dbamboo.home=/srv/bamboo/bamboo-home -Djdk.tls.ephemeralDHKeySize=2048 bamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL-JOB1 bamboo_planRepository_1_name=Jalview Git bamboo_buildKey=JB-GDL-JOB1 bamboo_shortPlanName=Getdown DEVELOP Launchers bamboo_repository_46497929_git_repositoryUrl=http://source.jalview.org/git/jalview.git bamboo_planRepository_name=Jalview Git LOGNAME=bamboo bamboo_buildNumber=74 PWD=/ bamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse bamboo_repository_46497929_branch_name=develop bamboo_shortJobName=Default Job bamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDL-JOB1-74 bamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git SHELL=/bin/bash bamboo_repository_46497929_previous_revision_number=1dad9dc2f7ff8466ad11d8c945aaa9140748ef8a bamboo_agentId=196609 bamboo_planName=Jalview Builds - Getdown DEVELOP Launchers bamboo_shortPlanKey=GDL bamboo_shortJobKey=JOB1 bamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk bamboo_planRepository_revision=1dad9dc2f7ff8466ad11d8c945aaa9140748ef8a bamboo_repository_46497929_git_username= bamboo_buildTimeStamp=2025-02-06T11:24:21.095Z bamboo_repository_previous_revision_number=1dad9dc2f7ff8466ad11d8c945aaa9140748ef8a bamboo_planRepository_previousRevision=1dad9dc2f7ff8466ad11d8c945aaa9140748ef8a bamboo_repository_46497929_revision_number=1dad9dc2f7ff8466ad11d8c945aaa9140748ef8a bamboo_repository_git_branch=develop bamboo_buildResultKey=JB-GDL-JOB1-74 bamboo_repository_branch_name=develop bamboo_buildPlanName=Jalview Builds - Getdown DEVELOP Launchers - Default Job bamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11 bamboo_planRepository_1_revision=1dad9dc2f7ff8466ad11d8c945aaa9140748ef8a SHLVL=1 bamboo_CHANNEL=DEVELOP bamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant bamboo_repository_name=Jalview Git JAVA_HOME=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk/ bamboo_dependenciesDisabled=false LANG=en_GB.UTF-8 bamboo_buildFailed=false bamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk bamboo_planRepository_branch=develop bamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609 bamboo_capability_system_git_executable=/bin/git bamboo_repository_git_username= bamboo_planRepository_1_previousRevision=1dad9dc2f7ff8466ad11d8c945aaa9140748ef8a bamboo_planRepository_branchDisplayName=develop bamboo_repository_46497929_name=Jalview Git bamboo_planRepository_1_type=gitv2 bamboo_planRepository_branchName=develop _=/usr/bin/java bamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11 bamboo_capability_system_builderivy_Ivy=/usr bamboo_plan_storageTag=plan-46301457 bamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle bamboo_hg_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_hg-repositories-cache bamboo_planRepository_1_username= bamboo_planRepository_type=gitv2 USER=bamboo bamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache bamboo_ManualBuildTriggerReason_userName=Soares bamboo_repository_git_repositoryUrl=http://source.jalview.org/git/jalview.git bamboo_repository_46497929_git_branch=develop bamboo_capability_system_builder_ant_Ant=/usr/share/ant bamboo_capability_system_builder_mvn3_Maven_3=/usr/share/maven bamboo_tmp_directory=/srv/bamboo/bamboo-home/temp bamboo_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL-JOB1 bamboo_planKey=JB-GDL bamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git bamboo_planRepository_username= HOME=/home/bamboo bamboo_planRepository_1_branchName=develop PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin |
| 06-Feb-2025 11:24:28 | Starting a Gradle Daemon (subsequent builds will be faster) |
| 06-Feb-2025 11:24:39 | |
| 06-Feb-2025 11:24:39 | > Configure project : |
| 06-Feb-2025 11:24:39 | Using properties from file './utils/channels/default/channel_gradle.properties' |
| 06-Feb-2025 11:24:39 | JALVIEW_VERSION is set to '2.11.4.2' |
| 06-Feb-2025 11:24:39 | HEADLESS BUILD |
| 06-Feb-2025 11:24:39 | J2S ENABLED |
| 06-Feb-2025 11:24:40 | Using a BUILD profile. |
| 06-Feb-2025 11:24:41 | eclipseDir exists |
| 06-Feb-2025 11:24:42 | |
| 06-Feb-2025 11:24:42 | > Task :clean |
| 06-Feb-2025 11:24:42 | > Task :cleanPackageDir |
| 06-Feb-2025 11:24:43 | > Task :getdownImagesCopy |
| 06-Feb-2025 11:24:43 | > Task :getdownImagesProcess |
| 06-Feb-2025 11:24:43 | > Task :getdownImages |
| 06-Feb-2025 11:24:46 | > Task :copyHelp |
| 06-Feb-2025 11:24:50 | > Task :buildIndices |
| 06-Feb-2025 11:24:50 | > Task :copyResources |
| 06-Feb-2025 11:24:51 | > Task :copyChannelResources |
| 06-Feb-2025 11:24:51 | |
| 06-Feb-2025 11:24:51 | > Task :createBuildProperties |
| 06-Feb-2025 11:24:51 | Execution optimizations have been disabled for task ':createBuildProperties' to ensure correctness due to the following reasons: |
| 06-Feb-2025 11:24:51 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL-JOB1/build/resources/resources_build'. Reason: Task ':createBuildProperties' uses this output of task ':copyChannelResources' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. |
| 06-Feb-2025 11:24:51 | |
| 06-Feb-2025 11:24:51 | > Task :buildResources |
| 06-Feb-2025 11:24:51 | > Task :copyDocs |
| 06-Feb-2025 11:24:52 | |
| 06-Feb-2025 11:24:52 | > Task :convertMdFiles |
| 06-Feb-2025 11:24:52 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL-JOB1/build/resources/doc_build/doc/README-DMG_creation.html |
| 06-Feb-2025 11:24:52 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL-JOB1/build/resources/doc_build/doc/releaseprocess.html |
| 06-Feb-2025 11:24:52 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL-JOB1/build/resources/doc_build/doc/README-DMG_background_image_creation.html |
| 06-Feb-2025 11:24:52 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL-JOB1/build/resources/doc_build/doc/building.html |
| 06-Feb-2025 11:24:52 | Creating /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL-JOB1/build/resources/doc_build/doc/jalview-projects.html |
| 06-Feb-2025 11:24:52 | |
| 06-Feb-2025 11:24:52 | > Task :releasesTemplates |
| 06-Feb-2025 11:24:52 | Execution optimizations have been disabled for task ':releasesTemplates' to ensure correctness due to the following reasons: |
| 06-Feb-2025 11:24:52 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL-JOB1/build/resources/help_build/help/html/releases.html'. Reason: Task ':buildIndices' uses this output of task ':releasesTemplates' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. |
| 06-Feb-2025 11:24:52 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL-JOB1/build/resources/help_build/help/html/whatsNew.html'. Reason: Task ':buildIndices' uses this output of task ':releasesTemplates' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. |
| 06-Feb-2025 11:24:52 | Stripping rc/test/etc for 2_11_4_2 |
| 06-Feb-2025 11:24:52 | Looking in /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL-JOB1/help/markdown/whatsnew/whatsnew-2_11_4_2.md |
| 06-Feb-2025 11:24:52 | |
| 06-Feb-2025 11:24:52 | > Task :prepare |
| 06-Feb-2025 11:24:54 | |
| 06-Feb-2025 11:24:54 | > Task :compileJava |
| 06-Feb-2025 11:24:54 | Setting target compatibility to 11 |
| 06-Feb-2025 11:25:14 | Note: Some input files use or override a deprecated API. |
| 06-Feb-2025 11:25:14 | Note: Recompile with -Xlint:deprecation for details. |
| 06-Feb-2025 11:25:14 | Note: Some input files use unchecked or unsafe operations. |
| 06-Feb-2025 11:25:14 | Note: Recompile with -Xlint:unchecked for details. |
| 06-Feb-2025 11:25:18 | |
| 06-Feb-2025 11:25:18 | > Task :processResources |
| 06-Feb-2025 11:25:18 | Execution optimizations have been disabled for task ':processResources' to ensure correctness due to the following reasons: |
| 06-Feb-2025 11:25:18 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL-JOB1/build/resources/doc_build'. Reason: Task ':processResources' uses this output of task ':convertMdFiles' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. |
| 06-Feb-2025 11:25:18 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL-JOB1/build/resources/doc_build'. Reason: Task ':processResources' uses this output of task ':copyDocs' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. |
| 06-Feb-2025 11:25:18 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL-JOB1/build/resources/help_build'. Reason: Task ':processResources' uses this output of task ':buildIndices' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. |
| 06-Feb-2025 11:25:18 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL-JOB1/build/resources/help_build'. Reason: Task ':processResources' uses this output of task ':copyHelp' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. |
| 06-Feb-2025 11:25:18 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL-JOB1/build/resources/help_build'. Reason: Task ':processResources' uses this output of task ':releasesTemplates' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. |
| 06-Feb-2025 11:25:18 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL-JOB1/build/resources/resources_build'. Reason: Task ':processResources' uses this output of task ':copyChannelResources' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. |
| 06-Feb-2025 11:25:18 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL-JOB1/build/resources/resources_build'. Reason: Task ':processResources' uses this output of task ':copyResources' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. |
| 06-Feb-2025 11:25:18 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL-JOB1/build/resources/resources_build'. Reason: Task ':processResources' uses this output of task ':createBuildProperties' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. |
| 06-Feb-2025 11:25:18 | |
| 06-Feb-2025 11:25:18 | > Task :classes |
| 06-Feb-2025 11:25:19 | |
| 06-Feb-2025 11:25:19 | > Task :compileLinkCheck |
| 06-Feb-2025 11:25:19 | Execution optimizations have been disabled for task ':compileLinkCheck' to ensure correctness due to the following reasons: |
| 06-Feb-2025 11:25:19 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL-JOB1/utils'. Reason: Task ':convertMdFiles' uses this output of task ':compileLinkCheck' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. |
| 06-Feb-2025 11:25:19 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL-JOB1/utils'. Reason: Task ':copyChannelResources' uses this output of task ':compileLinkCheck' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. |
| 06-Feb-2025 11:25:19 | - Gradle detected a problem with the following location: '/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL-JOB1/utils'. Reason: Task ':getdownImagesCopy' uses this output of task ':compileLinkCheck' without declaring an explicit or implicit dependency. This can lead to incorrect results being produced, depending on what order the tasks are executed. Please refer to https://docs.gradle.org/7.4.2/userguide/validation_problems.html#implicit_dependency for more details about this problem. |
| 06-Feb-2025 11:25:20 | |
| 06-Feb-2025 11:25:20 | > Task :linkCheck |
| 06-Feb-2025 11:25:20 | Checking help file links |
| 06-Feb-2025 11:25:20 | |
| 06-Feb-2025 11:25:20 | Results: |
| 06-Feb-2025 11:25:20 | 159 distinct help targets |
| 06-Feb-2025 11:25:20 | 159 help mappings |
| 06-Feb-2025 11:25:20 | 0 invalid targets |
| 06-Feb-2025 11:25:20 | 32 unused targets |
| 06-Feb-2025 11:25:20 | uniprotfetcher: html/features/uniprotsequencefetcher.html |
| 06-Feb-2025 11:25:20 | overviewprefs: html/features/preferences.html#overview |
| 06-Feb-2025 11:25:20 | cdnafeatures: html/features/codingfeatures.html |
| 06-Feb-2025 11:25:20 | startupprefs: html/features/preferences.html#startup |
| 06-Feb-2025 11:25:20 | ensemblfetch: html/features/ensemblsequencefetcher.html |
| 06-Feb-2025 11:25:20 | io.modellerpir: html/io/modellerpir.html |
| 06-Feb-2025 11:25:20 | structureandpaefromfile: html/features/structurechooser.html#loadfromfile |
| 06-Feb-2025 11:25:20 | pdbmcviewer: html/features/pdbviewer.html |
| 06-Feb-2025 11:25:20 | workingwithpae: html/features/paematrices.html |
| 06-Feb-2025 11:25:20 | groovy.colours: html/features/groovy.html#groovyColours |
| 06-Feb-2025 11:25:20 | seqmappings: html/features/seqmappings.html |
| 06-Feb-2025 11:25:20 | uniprotfts: html/features/uniprotsequencefetcher.html#uniprotfts |
| 06-Feb-2025 11:25:20 | splitframe.mirrorfonts: html/features/splitView.html#mirror |
| 06-Feb-2025 11:25:20 | subtMatrices.pam250: html/calculations/scorematrices.html#pam250 |
| 06-Feb-2025 11:25:20 | search: html/features/search.html |
| 06-Feb-2025 11:25:20 | viewingpdbs.reps: html/features/viewingpdbs.html#viewreps |
| 06-Feb-2025 11:25:20 | alformats: html/io/fileformats.html |
| 06-Feb-2025 11:25:20 | strucprefs: html/features/preferences.html#structure |
| 06-Feb-2025 11:25:20 | siftsmapping: html/features/siftsmapping.html |
| 06-Feb-2025 11:25:20 | chimera.annotxfer: html/features/chimera.html#annotxfer |
| 06-Feb-2025 11:25:20 | pdbfts: html/features/pdbsequencefetcher.html#pdbfts |
| 06-Feb-2025 11:25:20 | newkeys: html/features/newkeystrokes.html |
| 06-Feb-2025 11:25:20 | importvcf.attribs: html/features/importvcf.html#attribs |
| 06-Feb-2025 11:25:20 | seqfeatures.settings.selcols: html/features/featuresettings.html#selectbyfeature |
| 06-Feb-2025 11:25:20 | structuresvia3dbeacons: html/features/structurechooser.html#3dbeaconssearch |
| 06-Feb-2025 11:25:20 | jalarchive: html/features/jalarchive.html |
| 06-Feb-2025 11:25:20 | newsreader: html/webServices/newsreader.html |
| 06-Feb-2025 11:25:20 | jalviewcltool: html/features/commandline.html#script |
| 06-Feb-2025 11:25:20 | popMenuAddref: html/menus/popupMenu.html#addrefannot |
| 06-Feb-2025 11:25:20 | splitframe.virtualfeats: html/features/splitView.html#virtualfeats |
| 06-Feb-2025 11:25:20 | paematrixformat: html/io/paematrixformat.html |
| 06-Feb-2025 11:25:20 | overview: html/features/overview.html |
| 06-Feb-2025 11:25:20 | 0 invalid map urls |
| 06-Feb-2025 11:25:20 | 0 invalid image attributes |
| 06-Feb-2025 11:25:20 | 506 internal href links (110 with anchors) |
| 06-Feb-2025 11:25:20 | 0 invalid internal href links |
| 06-Feb-2025 11:25:20 | 0 invalid internal anchor links |
| 06-Feb-2025 11:25:20 | 112 external href links |
| 06-Feb-2025 11:25:20 | External links not verified as internet not available |
| 06-Feb-2025 11:25:20 | *** Success *** |
| 06-Feb-2025 11:25:21 | |
| 06-Feb-2025 11:25:21 | > Task :jar |
| 06-Feb-2025 11:25:22 | > Task :syncJars |
| 06-Feb-2025 11:25:22 | > Task :makeDist |
| 06-Feb-2025 11:25:23 | > Task :getdownWebsiteBuild |
| 06-Feb-2025 11:25:24 | |
| 06-Feb-2025 11:25:24 | > Task :getdownDigest |
| 06-Feb-2025 11:25:24 | Generating digest file './build/website/docroot/getdown/default/11/digest.txt'... |
| 06-Feb-2025 11:25:24 | Generating digest file './build/website/docroot/getdown/default/11/digest2.txt'... |
| 06-Feb-2025 11:25:24 | |
| 06-Feb-2025 11:25:24 | > Task :getdown |
| 06-Feb-2025 11:25:24 | |
| 06-Feb-2025 11:25:24 | Deprecated Gradle features were used in this build, making it incompatible with Gradle 8.0. |
| 06-Feb-2025 11:25:24 | |
| 06-Feb-2025 11:25:24 | You can use '--warning-mode all' to show the individual deprecation warnings and determine if they come from your own scripts or plugins. |
| 06-Feb-2025 11:25:24 | |
| 06-Feb-2025 11:25:24 | See https://docs.gradle.org/7.4.2/userguide/command_line_interface.html#sec:command_line_warnings |
| 06-Feb-2025 11:25:24 | |
| 06-Feb-2025 11:25:24 | Execution optimizations have been disabled for 4 invalid unit(s) of work during this build to ensure correctness. |
| 06-Feb-2025 11:25:24 | 2025/02/06 11:25:23:463 WARNING Starting without install4j classes |
| 06-Feb-2025 11:25:24 | 2025/02/06 11:25:24:011 WARNING Starting without install4j classes |
| 06-Feb-2025 11:25:24 | Please consult deprecation warnings for more details. |
| 06-Feb-2025 11:25:24 | |
| 06-Feb-2025 11:25:24 | BUILD SUCCESSFUL in 56s |
| 06-Feb-2025 11:25:24 | 21 actionable tasks: 21 executed |
| 06-Feb-2025 11:25:25 | Finished task 'Jalview Develop Launcher JVL (Java 11)' with result: Success |
| 06-Feb-2025 11:25:25 | Starting task 'Copy JVL file and produce link in HTML' of type 'com.atlassian.bamboo.plugins.scripttask:task.builder.script' |
| 06-Feb-2025 11:25:25 | Beginning to execute external process for build 'Jalview Builds - Getdown DEVELOP Launchers - Default Job #74 (JB-GDL-JOB1-74)' ... running command line: /srv/bamboo/bamboo-home/temp/JB-GDL-JOB1-74-ScriptBuildTask-943704048014558486.sh ... in: /srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL-JOB1 ... using extra environment variables: bamboo_planRepository_1_branch=develop bamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr bamboo_planRepository_1_branchDisplayName=develop bamboo_repository_revision_number=1dad9dc2f7ff8466ad11d8c945aaa9140748ef8a bamboo_resultsUrl=https://builds.jalview.org/browse/JB-GDL-JOB1-74 bamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL-JOB1 bamboo_planRepository_1_name=Jalview Git bamboo_buildKey=JB-GDL-JOB1 bamboo_shortPlanName=Getdown DEVELOP Launchers bamboo_repository_46497929_git_repositoryUrl=http://source.jalview.org/git/jalview.git bamboo_planRepository_name=Jalview Git bamboo_buildNumber=74 bamboo_capability_system_builder_command_Eclipse_2019_09=/home/bamboo/buildtools/eclipse/jee-2019-09/eclipse/eclipse bamboo_repository_46497929_branch_name=develop bamboo_shortJobName=Default Job bamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-GDL-JOB1-74 bamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git bamboo_repository_46497929_previous_revision_number=1dad9dc2f7ff8466ad11d8c945aaa9140748ef8a bamboo_agentId=196609 bamboo_planName=Jalview Builds - Getdown DEVELOP Launchers bamboo_shortPlanKey=GDL bamboo_shortJobKey=JOB1 bamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jdk/jdk-11-linux-x64/jdk bamboo_planRepository_revision=1dad9dc2f7ff8466ad11d8c945aaa9140748ef8a bamboo_repository_46497929_git_username= bamboo_buildTimeStamp=2025-02-06T11:24:21.095Z bamboo_repository_previous_revision_number=1dad9dc2f7ff8466ad11d8c945aaa9140748ef8a bamboo_planRepository_previousRevision=1dad9dc2f7ff8466ad11d8c945aaa9140748ef8a bamboo_repository_46497929_revision_number=1dad9dc2f7ff8466ad11d8c945aaa9140748ef8a bamboo_repository_git_branch=develop bamboo_buildResultKey=JB-GDL-JOB1-74 bamboo_repository_branch_name=develop bamboo_buildPlanName=Jalview Builds - Getdown DEVELOP Launchers - Default Job bamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11 bamboo_planRepository_1_revision=1dad9dc2f7ff8466ad11d8c945aaa9140748ef8a bamboo_CHANNEL=DEVELOP bamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant bamboo_repository_name=Jalview Git bamboo_build_commandline_org_jfrog_bamboo_bamboo_artifactory_plugin_artifactoryGradleTask_2=/home/bamboo/buildtools/gradle/bin/gradle -x test -PCHANNEL=BUILD -PJAVA_VERSION=11 -Pbamboo_planKey=JB-GDL -Pbamboo_buildResultsUrl=${bamboo_buildResultsUrl} -Pbamboo_buildResultKey=${bamboo_buildResultKey} clean getdown bamboo_dependenciesDisabled=false bamboo_buildFailed=false bamboo_capability_system_jdk_OpenJDK_8=/home/bamboo/buildtools/jdk/jdk-8-linux-x64/jdk bamboo_planRepository_branch=develop bamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609 bamboo_capability_system_git_executable=/bin/git bamboo_repository_git_username= bamboo_planRepository_1_previousRevision=1dad9dc2f7ff8466ad11d8c945aaa9140748ef8a bamboo_planRepository_branchDisplayName=develop bamboo_repository_46497929_name=Jalview Git bamboo_planRepository_1_type=gitv2 bamboo_planRepository_branchName=develop bamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11 bamboo_capability_system_builderivy_Ivy=/usr bamboo_plan_storageTag=plan-46301457 bamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle bamboo_hg_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_hg-repositories-cache bamboo_planRepository_1_username= bamboo_planRepository_type=gitv2 bamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache bamboo_ManualBuildTriggerReason_userName=Soares bamboo_repository_git_repositoryUrl=http://source.jalview.org/git/jalview.git bamboo_repository_46497929_git_branch=develop bamboo_capability_system_builder_ant_Ant=/usr/share/ant bamboo_capability_system_builder_mvn3_Maven_3=/usr/share/maven bamboo_tmp_directory=/srv/bamboo/bamboo-home/temp bamboo_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/196609/JB-GDL-JOB1 bamboo_planKey=JB-GDL bamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git bamboo_planRepository_username= bamboo_planRepository_1_branchName=develop |
| 06-Feb-2025 11:25:25 | Finished task 'Copy JVL file and produce link in HTML' with result: Success |
| 06-Feb-2025 11:25:25 | Running post build plugin 'NCover Results Collector' |
| 06-Feb-2025 11:25:25 | Running post build plugin 'Artifact Copier' |
| 06-Feb-2025 11:25:25 | Publishing an artifact: getdown |
| 06-Feb-2025 11:25:25 | Finished publishing of artifact Shared artifact: [getdown], pattern: [**/*] anchored at: [build/website/docroot/getdown/default/11] in 97.95 ms |
| 06-Feb-2025 11:25:25 | Running post build plugin 'Artifactory Release Management Staging' |
| 06-Feb-2025 11:25:25 | Running post build plugin 'Artifactory Build Info Copier' |
| 06-Feb-2025 11:25:25 | Running post build plugin 'Artifactory Gradle Properties Info Copier' |
| 06-Feb-2025 11:25:25 | Running post build plugin 'npm Cache Cleanup' |
| 06-Feb-2025 11:25:25 | Running post build plugin 'Clover Results Collector' |
| 06-Feb-2025 11:25:25 | Running post build plugin 'Docker Container Cleanup' |
| 06-Feb-2025 11:25:25 | Finalising the build... |
| 06-Feb-2025 11:25:25 | Stopping timer. |
| 06-Feb-2025 11:25:25 | Build JB-GDL-JOB1-74 completed. |
| 06-Feb-2025 11:25:25 | Running on server: post build plugin 'NCover Results Collector' |
| 06-Feb-2025 11:25:25 | Running on server: post build plugin 'Build Hanging Detection Configuration' |
| 06-Feb-2025 11:25:25 | Running on server: post build plugin 'Clover Delta Calculator' |
| 06-Feb-2025 11:25:25 | Running on server: post build plugin 'Maven Dependencies Postprocessor' |
| 06-Feb-2025 11:25:25 | All post build plugins have finished |
| 06-Feb-2025 11:25:25 | Generating build results summary... |
| 06-Feb-2025 11:25:25 | Saving build results to disk... |
| 06-Feb-2025 11:25:25 | Logging substituted variables... |
| 06-Feb-2025 11:25:25 | Indexing build results... |
| 06-Feb-2025 11:25:25 | Finished building JB-GDL-JOB1-74. |